Figure S1 scRNAseq of CD34+Lin- hematopoietic stem and progenitor cells (HSPCs) and cell type annotation.
load the library and object
library(SingCellaR)
library(ggplot2)

load(file = "/Users/gwang/DBA/DBA_revision/Objects/DBA_harmony.rdata")
A) Aggregate of 41,415 cells from 9 individual donors, after regression of donor effect. Single cells are colored by sample ID and donor type (healthy control, RPS-DBA or RPL-DBA).
By sampleID
res.umap <- DBA@umap.result

p <- qplot(UMAP1,UMAP2, data=res.umap,colour=sampleID) + geom_point(size=0.1) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),panel.background = element_blank(), axis.line = element_line(colour = "black"))  +  theme_void() + theme(legend.position="none")
p

By donor type
res.umap <- DBA@umap.result

p <- qplot(UMAP1,UMAP2, data=res.umap,colour=genotype) + geom_point(size=0.1)+ scale_color_manual(values=c("orange", "red","cyan")) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),panel.background = element_blank(), axis.line = element_line(colour = "black"))  +  theme_void() + theme(legend.position="none")
p

B) The heatmap shows the top 8 top upregulated genes in 19 clusters generated by Louvain community-detection clustering method. Legend shows Z-score of expression.
plot_heatmap_for_marker_genes(DBA,cluster.type = "louvain",isClusterByRow = F,
                              n.TopGenes = 8,min.log2FC = 0.5,min.expFraction = 0.3,
                              rowFont.size = 5,split.line.col = "white")